In a fitting finale for the hosts to the four-day diving program, Bedggood, 23, finished with 451.15 points ahead of Dixon (449.55) while Canada's Vincent Riendeau (425.40pts) took bronze.
Overall Australia claimed three gold, three silver and five bronze – an improvement on Glasgow 2014's two gold, three silver and three bronze.
Australia finished second behind England (four gold, three silver, one bronze) on the Gold Coast diving table.
"I thought 'that was it, I blew it'. It was my final dive and it was supposed to be my best dive," Bedggood said.
"When the score came up I was like in disbelief.
"But that's the highs and lows of the competition. It is more of a mental game than a diving game sometimes.
"I am ecstatic with gold but performance-wise I was not overly happy. There are things that I definitely need to improve on."
Remarkably Bedggood had to rely on special consideration just to make the Games team after missing trials with a leg injury.
"That was a bit of an anxious wait but I felt I had done enough in the past to be worthy of being on the team – I am glad they picked me," he smiled.
Earlier, Australia's Maddison Keeney claimed silver in the women's 3m springboard final with teammate Anabelle Smith taking bronze.
